Summary of the bioinformatic pipeline

Code

library(knitr)
library(targets)
library(MiscMetabar)

Le chargement a nécessité le package : phyloseq

Le chargement a nécessité le package : ggplot2

Le chargement a nécessité le package : dada2

Le chargement a nécessité le package : Rcpp

Le chargement a nécessité le package : dplyr


Attachement du package : 'dplyr'

Les objets suivants sont masqués depuis 'package:stats':

    filter, lag

Les objets suivants sont masqués depuis 'package:base':

    intersect, setdiff, setequal, union

Le chargement a nécessité le package : purrr

Code

tar_visnetwork(script=here::here("_targets.R"))

Le chargement a nécessité le package : phyloseq
Le chargement a nécessité le package : ggplot2
Le chargement a nécessité le package : dada2
Le chargement a nécessité le package : Rcpp
Le chargement a nécessité le package : dplyr

Attachement du package : ‘dplyr’

Les objets suivants sont masqués depuis ‘package:stats’:

    filter, lag

Les objets suivants sont masqués depuis ‘package:base’:

    intersect, setdiff, setequal, union

Le chargement a nécessité le package : purrr
here() starts at /home/adrien/Nextcloud/IdEst/Projets/arround_MiscMetabar/bioinfo.starter
here() starts at /home/adrien/Nextcloud/IdEst/Projets/arround_MiscMetabar/bioinfo.starter

Load phyloseq object from targets store

Code

#tar_load()

The {targets} package is at the core of this project. Please read the intro of the user manual if you don’t know {targets}.

The {targets} package store … targets in a folder and can load (tar_load()) and read (tar_read) object from this folder.

Sample data

Code

DT::datatable(data_fungi@sam_data)

Session Information

Session information are detailed below. More information about the machine, the system, as well as python and R packages, are available in the file data_final/information_run.txt.

Code

sessionInfo()

R version 4.4.1 (2024-06-14)
Platform: x86_64-pc-linux-gnu
Running under: Debian GNU/Linux 12 (bookworm)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.11.0 
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.11.0

locale:
 [1] LC_CTYPE=fr_FR.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=fr_FR.UTF-8        LC_COLLATE=fr_FR.UTF-8    
 [5] LC_MONETARY=fr_FR.UTF-8    LC_MESSAGES=fr_FR.UTF-8   
 [7] LC_PAPER=fr_FR.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=fr_FR.UTF-8 LC_IDENTIFICATION=C       

time zone: Europe/Paris
tzcode source: system (glibc)

attached base packages:
[1] stats     graphics  grDevices datasets  utils     methods   base     

other attached packages:
[1] MiscMetabar_0.9.3 purrr_1.0.2       dplyr_1.1.4       dada2_1.32.0     
[5] Rcpp_1.0.13       ggplot2_3.5.1     phyloseq_1.48.0   targets_1.8.0    
[9] knitr_1.48       

loaded via a namespace (and not attached):
  [1] bitops_1.0-9                deldir_2.0-4               
  [3] permute_0.9-7               rlang_1.1.4                
  [5] magrittr_2.0.3              ade4_1.7-22                
  [7] matrixStats_1.4.1           compiler_4.4.1             
  [9] mgcv_1.9-1                  png_0.1-8                  
 [11] callr_3.7.6                 vctrs_0.6.5                
 [13] reshape2_1.4.4              stringr_1.5.1              
 [15] pwalign_1.0.0               pkgconfig_2.0.3            
 [17] crayon_1.5.3                fastmap_1.2.0              
 [19] backports_1.5.0             XVector_0.44.0             
 [21] utf8_1.2.4                  Rsamtools_2.20.0           
 [23] rmarkdown_2.28              UCSC.utils_1.0.0           
 [25] ps_1.8.0                    xfun_0.48                  
 [27] cachem_1.1.0                zlibbioc_1.50.0            
 [29] GenomeInfoDb_1.40.1         jsonlite_1.8.9             
 [31] biomformat_1.32.0           rhdf5filters_1.16.0        
 [33] DelayedArray_0.30.1         Rhdf5lib_1.26.0            
 [35] BiocParallel_1.38.0         jpeg_0.1-10                
 [37] parallel_4.4.1              cluster_2.1.6              
 [39] R6_2.5.1                    bslib_0.8.0                
 [41] RColorBrewer_1.1-3          stringi_1.8.4              
 [43] jquerylib_0.1.4             GenomicRanges_1.56.1       
 [45] SummarizedExperiment_1.34.0 iterators_1.0.14           
 [47] IRanges_2.38.1              Matrix_1.7-0               
 [49] splines_4.4.1               igraph_2.0.3               
 [51] tidyselect_1.2.1            rstudioapi_0.16.0          
 [53] abind_1.4-8                 yaml_2.3.10                
 [55] vegan_2.6-8                 codetools_0.2-20           
 [57] hwriter_1.3.2.1             processx_3.8.4             
 [59] lattice_0.22-6              tibble_3.2.1               
 [61] plyr_1.8.9                  Biobase_2.64.0             
 [63] withr_3.0.1                 ShortRead_1.62.0           
 [65] evaluate_1.0.0              survival_3.7-0             
 [67] RcppParallel_5.1.9          Biostrings_2.72.1          
 [69] pillar_1.9.0                BiocManager_1.30.25        
 [71] MatrixGenerics_1.16.0       DT_0.33                    
 [73] renv_1.0.9                  foreach_1.5.2              
 [75] stats4_4.4.1                generics_0.1.3             
 [77] rprojroot_2.0.4             S4Vectors_0.42.1           
 [79] munsell_0.5.1               scales_1.3.0               
 [81] base64url_1.4               glue_1.8.0                 
 [83] tools_4.4.1                 interp_1.1-6               
 [85] data.table_1.16.0           GenomicAlignments_1.40.0   
 [87] visNetwork_2.1.2            rhdf5_2.48.0               
 [89] grid_4.4.1                  ape_5.8                    
 [91] crosstalk_1.2.1             latticeExtra_0.6-30        
 [93] colorspace_2.1-1            nlme_3.1-166               
 [95] GenomeInfoDbData_1.2.12     cli_3.6.3                  
 [97] fansi_1.0.6                 S4Arrays_1.4.1             
 [99] gtable_0.3.5                sass_0.4.9                 
[101] digest_0.6.37               BiocGenerics_0.50.0        
[103] SparseArray_1.4.8           htmlwidgets_1.6.4          
[105] htmltools_0.5.8.1           multtest_2.60.0            
[107] lifecycle_1.0.4             here_1.0.1                 
[109] httr_1.4.7                  secretbase_1.0.3           
[111] MASS_7.3-61